Yes, this is a problem. I'm not sure NAT is the solution, though. I mean, if you're going to use NAT, why switch to IPv6 in the first place?
reasons will vary from "because my vendors are pushing it" to "because it has some feature that makes my life easier" to "because some application my users are asking for only works on ipv6" to "because it will help me justify next year's IT budget". one reason that won't be on the list is "because i cannot otherwise get enough address space to become fully locked into my current transit provider."
Unless I'm very much mistaken, this transition mechanism ("NAT-PT") translates from IPv6 to IPv4 and vice versa, NOT from IPv6 to IPv6.
sure, but abusing tools for purposes other than what they were made for is how most IT directors earn their salaries (though they don't call it that.) and i don't imagine the site-local address ranges will be given to a RIR, so folks who decide to number their enterprise in that range and then speak to "the internet" through an as-yet-unannounced ipv6-nat product will just do that.
... we'll still have the age-old tension between "i could get global routing for that address block" and "i could qualify with my RIR to obtain that address block (and afford the fees)".
IETF multi6 wg is working on this problem. Hopefully it's possible to come up with something that offers both scalability and functionality, as current PI and PA paradigms each only offer one.
as someone who cared deeply about this at one time and who watched A6/DNAME become a fly on the windshield of ietf backroom politics, i wish you luck. it's important to remember that large network owners don't care about this, and they are the ones who tell the vendors what to build. someone who wants to build a 3G network doesn't want A6/DNAME or any other added complexity adding logic and bugs to their handhelds or their cell towers. someone who wants to sell a lot of business-DSL is happier if their customers are locked in. so exactly where the multi6 group is planning to sell their results, i can't imagine.